Protein Structure Analysis — Pipeline Skill (Thin Scaffold)

Overview

Adds tool-selection logic, format-conversion rules, and niche gotchas for protein structure tasks. The agent already knows Biopython/PyMOL syntax — this skill prevents common parameter and workflow mistakes.

Usage

• Activate when parsing PDB/mmCIF, computing RMSD, detecting pockets, or converting formats
• Activate for Ramachandran plots, contact maps, B-factor analysis, or DSSP assignment
• Activate when preparing structures for downstream docking (PDBQT export)

Core Concepts

SMCRA hierarchy: Structure → Model → Chain → Residue → Atom. Always iterate at the correct level; NMR files have multiple models.

Altloc: Alternate conformations flagged with non-blank code ('A','B'). Filter to one before any geometry calculation.

fpocket output: Writes <basename>_out/ in the current working directory, not next to the input file. Pockets ranked by druggability score (0–1).

Decision Logic

Tool Selection

Task	Tool	Key consideration
Parse PDB/mmCIF	Biopython PDBParser/MMCIFParser	Always pass QUIET=True
RMSD superposition	Bio.PDB.Superimposer	Requires equal-length, 1-to-1 atom lists
Binding pocket detection	fpocket CLI	Needs clean PDB (no altloc, no HETATM clutter)
Pocket visualization	PyMOL (-cq for headless)	byres all within 5 of organic for pocket selection
Contact analysis	Bio.PDB.NeighborSearch	4.0 Å default cutoff; returns atom pairs
Secondary structure	DSSP via Biopython	Binary is mkdssp on newer installs
Format: PDB→mmCIF	Bio.PDB.MMCIFIO	Lossless for coordinates
Format: PDB→PDBQT	obabel -O out.pdbqt -xr	Add -xh for hydrogens first
Ramachandran	PPBuilder → get_phi_psi_list()	Termini return None — must check

RMSD Type Selection

Scenario	Atoms to use	Notes
Backbone comparison	Cα only	Standard for fold similarity
Loop flexibility	All backbone (N, Cα, C, O)	Captures local deviations
Binding site comparison	All-atom within 5 Å of ligand	Requires residue selection first
Identical sequences	All-atom	Only valid for same-length chains

Critical Parameters

Parameter	Value	When to change
NeighborSearch cutoff	4.0 Å	3.5 for H-bonds, 5.0 for hydrophobic
Superimposer atoms	Cα	All-atom only for identical sequences
fpocket -m (min alpha spheres)	35 (default)	Lower to 15 for small/shallow pockets
DSSP binary name	mkdssp	Use dssp on legacy installs
obabel -xr flag	receptor mode	Omit for flexible ligand PDBQT
PPBuilder vs CaPPBuilder	PPBuilder	CaPPBuilder only for Cα-only traces

Common Mistakes

• Wrong: Assuming single model in PDB → Right: Always structure[0] or iterate models → Why: NMR ensembles have many models; raw iteration hits unexpected atoms

• Wrong: Ignoring altloc in geometry → Right: Filter atom.get_altloc() in ('', 'A') → Why: Duplicate atoms corrupt RMSD and dihedral calculations

• Wrong: All-atom RMSD when backbone intended → Right: Restrict to Cα for fold comparison → Why: Side-chains inflate RMSD and break correspondence across non-identical sequences

• Wrong: Unequal-length atom lists in Superimposer → Right: Match by residue number, build parallel lists of equal length → Why: set_atoms() requires strict 1-to-1 correspondence

• Wrong: No hydrogens before PDBQT export → Right: obabel -xh then -xr -O receptor.pdbqt → Why: Crystal PDBs lack H; docking scoring needs them

• Wrong: Including HETATM/water in backbone calculations → Right: Filter residue.id[0] == ' ' → Why: Heteroatoms and water corrupt phi/psi and backbone RMSD

• Wrong: math.degrees() on None phi/psi → Right: Check if phi is not None and psi is not None → Why: Chain termini return None; TypeError crashes

• Wrong: Default dssp binary name → Right: Pass dssp='mkdssp' to DSSP() → Why: Newer installs only provide mkdssp

• Wrong: Expecting fpocket output next to input → Right: Run from target directory or move output after → Why: fpocket writes to CWD, not input file location

• Wrong: Forgetting QUIET=True in parser → Right: PDBParser(QUIET=True) → Why: Non-fatal warnings flood stdout and obscure real errors

Response Format

• Lead with the command or code the user needs — explain after
• Structure as: confirm inputs → working code → key parameters explained → gotchas
• One complete working example per task; do not show every alternative
• Keep code comments minimal and functional
• Target: 50-100 lines of code with brief surrounding explanation